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Conserved domains on  [gi|347546335|gb|AEP03289|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (plastid) [uncultured marine phototrophic eukaryote]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RuBisCO_large super family cl08232
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-124 1.92e-93

Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions.


The actual alignment was detected with superfamily member CHL00040:

Pssm-ID: 471793  Cd Length: 475  Bit Score: 276.97  E-value: 1.92e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335   1 ARDLGVPIVMHDYLTGGFTANTSLANYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTVVGKLE 80
Cdd:CHL00040 257 ARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLE 336

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 347546335  81 GEREVTLGFVDLMRDAYIEKDRSRGVYFTQDWCGLAGTMPVASG 124
Cdd:CHL00040 337 GEREMTLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVLPVASG 380
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-124 1.92e-93

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit


Pssm-ID: 176981  Cd Length: 475  Bit Score: 276.97  E-value: 1.92e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335   1 ARDLGVPIVMHDYLTGGFTANTSLANYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTVVGKLE 80
Cdd:CHL00040 257 ARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLE 336

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 347546335  81 GEREVTLGFVDLMRDAYIEKDRSRGVYFTQDWCGLAGTMPVASG 124
Cdd:CHL00040 337 GEREMTLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVLPVASG 380
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-124 2.41e-80

Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form I is the most abundant class, present in plants, algae, and bacteria, and forms large complexes composed of 8 large and 8 small subunits.


Pssm-ID: 173977  Cd Length: 450  Bit Score: 242.72  E-value: 2.41e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335   1 ARDLGVPIVMHDYLTGgFTANTSLANYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTVVGKLE 80
Cdd:cd08212  235 AKELGSPIIMHDLLTG-FTAIQSLAKWCRDNGMLLHLHRAGHATYDRQKNHGIHFRVLAKWLRLSGVDHIHAGTVVGKLE 313

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 347546335  81 GEREVTLGFVDLMRDAYIEKDRSRGVYFTQDWCGLAGTMPVASG 124
Cdd:cd08212  314 GDPLVTLGFYDLLRDDYIEKDRSRGIFFTQDWASLPGVMPVASG 357
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 1-124 9.19e-54

Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.


Pssm-ID: 459631  Cd Length: 292  Bit Score: 169.85  E-value: 9.19e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335    1 ARDLGVPIVMHDYLTGGFTANTSLANYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTV-VGKL 79
Cdd:pfam00016 103 AKETGGVAVMVDGLVIGPTAITTLRRWFRDNGVILHYHRAGHGAVTRQSKHGISFRVLAKMARLAGADHLHTGTMgVGKL 182

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 347546335   80 EGEREVTLgfvdlmRDAYIEKDRSRGVYFTQDWCGLAGTMPVASG 124
Cdd:pfam00016 183 EGDPSDTL------RAYMLEEDRARGPFFDQDWGGMPAVMPVASG 221
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-124 2.62e-36

Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate transport and metabolism];


Pssm-ID: 441455  Cd Length: 417  Bit Score: 127.59  E-value: 2.62e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335   1 ARDLGVPIVMHDYLTGGFTANTSLANycRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTVVGKLE 80
Cdd:COG1850  236 AVELGANAVMVDVNTVGLSAVQTLRE--EHIGLPIHAHRAGHGAFTRSPLHGISMRVLAKLWRLAGADHLHVGTPVGKME 313

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 347546335  81 GEREVTLGFVDLMRdayiekdrsrgvyftQDWCGLAGTMPVASG 124
Cdd:COG1850  314 GDDEEVLAIADALL---------------QPWGGLKPVFPVPSG 342
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 3-124 1.36e-25

ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, single chain, type III form of ribulose bisphosphate carboxylase, or RuBisCO. Members act is a three-step pathway for conversion of the sugar moiety of AMP to two molecules of 3-phosphoglycerate. Many of these species use ADP-dependent sugar kinases, which form AMP, for glycolysis. [Energy metabolism, Sugars]


Pssm-ID: 188307  Cd Length: 411  Bit Score: 99.08  E-value: 1.36e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335    3 DLGVPIVMHDYLTGGFTANTSLANYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTV-VGKLEG 81
Cdd:TIGR03326 234 DLGGEYVMVDIVVAGWSALQYVRERTEDLGLAIHAHRAMHAAFTRNPKHGISMFVLAKLYRLIGVDQLHTGTAgVGKLEG 313

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 347546335   82 EREVTLGFVDLMRdayiekdrsrgvyftQDWCGLAGTMPVASG 124
Cdd:TIGR03326 314 GNEDTKGINDFLR---------------QDWHHIKPVFPVASG 341
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-124 1.92e-93

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit


Pssm-ID: 176981  Cd Length: 475  Bit Score: 276.97  E-value: 1.92e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335   1 ARDLGVPIVMHDYLTGGFTANTSLANYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTVVGKLE 80
Cdd:CHL00040 257 ARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLE 336

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 347546335  81 GEREVTLGFVDLMRDAYIEKDRSRGVYFTQDWCGLAGTMPVASG 124
Cdd:CHL00040 337 GEREMTLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVLPVASG 380
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-124 2.41e-80

Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form I is the most abundant class, present in plants, algae, and bacteria, and forms large complexes composed of 8 large and 8 small subunits.


Pssm-ID: 173977  Cd Length: 450  Bit Score: 242.72  E-value: 2.41e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335   1 ARDLGVPIVMHDYLTGgFTANTSLANYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTVVGKLE 80
Cdd:cd08212  235 AKELGSPIIMHDLLTG-FTAIQSLAKWCRDNGMLLHLHRAGHATYDRQKNHGIHFRVLAKWLRLSGVDHIHAGTVVGKLE 313

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 347546335  81 GEREVTLGFVDLMRDAYIEKDRSRGVYFTQDWCGLAGTMPVASG 124
Cdd:cd08212  314 GDPLVTLGFYDLLRDDYIEKDRSRGIFFTQDWASLPGVMPVASG 357
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-124 1.17e-75

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 231.33  E-value: 1.17e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335   1 ARDLGVPIVMHDYLTGGFTANTSLANYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTVVGKLE 80
Cdd:PRK04208 250 AKELGSPIVMIDVVTAGWTALQSLREWCRDNGLALHAHRAMHAAFTRNPNHGISFRVLAKLLRLIGVDHLHTGTVVGKLE 329

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 347546335  81 GEREVTLGFVDLMRDAYIEKDRSRGVYFTQDWCGLAGTMPVASG 124
Cdd:PRK04208 330 GDRAEVLGYYDILREDFVPEDRSRGIFFDQDWGSIKPVFPVASG 373
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 1-124 5.56e-65

Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubico-like proteins (RLP), are missing critical active site residues.


Pssm-ID: 173971  Cd Length: 414  Bit Score: 202.47  E-value: 5.56e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335   1 ARDLGVPIVMHDYLTGGFTANTSLANYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTVVGKLE 80
Cdd:cd08206  222 AKELGSVIVMVDGVTAGWTAIQSARRWCPDNGLALHAHRAGHAAFTRQKNHGISMRVLAKLARLIGVDHIHTGTVVGKLE 301

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 347546335  81 GEREVTLGFVDLMRDAYIEKDRSRgVYFTQDWCGLAGTMPVASG 124
Cdd:cd08206  302 GDPSEVKGIADMLREDEVEGDLSR-IFFNQDWGGMKPVFPVASG 344
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 1-124 9.19e-54

Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.


Pssm-ID: 459631  Cd Length: 292  Bit Score: 169.85  E-value: 9.19e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335    1 ARDLGVPIVMHDYLTGGFTANTSLANYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTV-VGKL 79
Cdd:pfam00016 103 AKETGGVAVMVDGLVIGPTAITTLRRWFRDNGVILHYHRAGHGAVTRQSKHGISFRVLAKMARLAGADHLHTGTMgVGKL 182

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 347546335   80 EGEREVTLgfvdlmRDAYIEKDRSRGVYFTQDWCGLAGTMPVASG 124
Cdd:pfam00016 183 EGDPSDTL------RAYMLEEDRARGPFFDQDWGGMPAVMPVASG 221
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-124 5.18e-45

Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions.


Pssm-ID: 173969  Cd Length: 366  Bit Score: 149.50  E-value: 5.18e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335   1 ARDLGVPIVMHDYLTGGFTANTSLANYCRdNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTVVGKLE 80
Cdd:cd08148  216 ALELGANMLMVDVLTAGFSALQALAEDFE-IDLPIHVHRAMHGAVTRSKFHGISMLVLAKLLRMAGGDFIHTGTVVGKMA 294

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 347546335  81 GEREVTLGFVDLMRDayiekdrsrgvyftqDWCGLAGTMPVASG 124
Cdd:cd08148  295 LEREEALGIADALTD---------------DWAGFKRVFPVASG 323
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-124 2.62e-36

Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate transport and metabolism];


Pssm-ID: 441455  Cd Length: 417  Bit Score: 127.59  E-value: 2.62e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335   1 ARDLGVPIVMHDYLTGGFTANTSLANycRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTVVGKLE 80
Cdd:COG1850  236 AVELGANAVMVDVNTVGLSAVQTLRE--EHIGLPIHAHRAGHGAFTRSPLHGISMRVLAKLWRLAGADHLHVGTPVGKME 313

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 347546335  81 GEREVTLGFVDLMRdayiekdrsrgvyftQDWCGLAGTMPVASG 124
Cdd:COG1850  314 GDDEEVLAIADALL---------------QPWGGLKPVFPVPSG 342
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 3-124 5.59e-34

Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form III is only found in archaea and forms large subunit oligomers (dimers or decamers) that do not include small subunits.


Pssm-ID: 173978  Cd Length: 412  Bit Score: 121.73  E-value: 5.59e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335   3 DLGVPIVMHDYLTGGFTANTSLANYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTVVGKLEGE 82
Cdd:cd08213  222 DLGGKYVMIDVVVAGWSALQYLRDLAEDYGLAIHAHRAMHAAFTRNPRHGISMLVLAKLYRLIGVDQLHIGTAVGKMEGD 301

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 347546335  83 REVTLGFVDLMRDAYIEKDrSRGVYFTQDWCGLAGTMPVASG 124
Cdd:cd08213  302 KEEVLRIADILREQKYKPD-EEDFHLAQDWGGIKPVFPVASG 342
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 3-124 1.36e-25

ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, single chain, type III form of ribulose bisphosphate carboxylase, or RuBisCO. Members act is a three-step pathway for conversion of the sugar moiety of AMP to two molecules of 3-phosphoglycerate. Many of these species use ADP-dependent sugar kinases, which form AMP, for glycolysis. [Energy metabolism, Sugars]


Pssm-ID: 188307  Cd Length: 411  Bit Score: 99.08  E-value: 1.36e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335    3 DLGVPIVMHDYLTGGFTANTSLANYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTV-VGKLEG 81
Cdd:TIGR03326 234 DLGGEYVMVDIVVAGWSALQYVRERTEDLGLAIHAHRAMHAAFTRNPKHGISMFVLAKLYRLIGVDQLHTGTAgVGKLEG 313

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 347546335   82 EREVTLGFVDLMRdayiekdrsrgvyftQDWCGLAGTMPVASG 124
Cdd:TIGR03326 314 GNEDTKGINDFLR---------------QDWHHIKPVFPVASG 341
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
13-124 5.38e-13

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 63.97  E-value: 5.38e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335  13 YLTGGFTANTSLANYCRDN--GLLLHIHRAMHAVIDRQRN-HGIHFRVLTKALRMSGGDHLHSGTV-VGKLEGEREvtlg 88
Cdd:PRK13475 260 FLVDGYVAGPGAVTTARRQypDQYLHYHRAGHGAVTSPSSkRGYTAFVLSKMARLQGASGIHTGTMgYGKMEGEAD---- 335

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 347546335  89 fvDLMRDAYIEKDRSRGVYFTQDWCGLAGTMPVASG 124
Cdd:PRK13475 336 --DRVIAYMIERDSAQGPFYHQEWYGMKPTTPIISG 369
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 12-124 2.21e-11

Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form II is mainly found in bacteria, and forms large subunit oligomers (dimers, tetramers, etc.) that do not include small subunits.


Pssm-ID: 173976  Cd Length: 439  Bit Score: 59.44  E-value: 2.21e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335  12 DYLTGGFTANTSLANYCRDNglLLHIHRAMHAVIDRQRNH-GIHFRVLTKALRMSGGDHLHSGTV-VGKLEGEREvtlgf 89
Cdd:cd08211  262 DGYVAGPAAVTTARRRFPDQ--FLHYHRAGHGAVTSPQSKrGYTAFVLSKMARLQGASGIHTGTMgFGKMEGESS----- 334

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 347546335  90 vDLMRDAYIEKDRSRGVYFTQDWCGLAGTMPVASG 124
Cdd:cd08211  335 -DKVIAYMIERDEAQGPLFNQKWYGMKPTTPIISG 368
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 1-124 2.54e-07

Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions, like for example 2,3-diketo-5-methylthiopentyl-1-phosphate enolase or 5-methylthio-d-ribulose 1-phosphate isomerase.


Pssm-ID: 173970  Cd Length: 367  Bit Score: 47.53  E-value: 2.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347546335   1 ARDLGVPIVMHDYLTGGFTANTSLAnycRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLHSGTVVGKLE 80
Cdd:cd08205  219 AVEAGANALLINPNLVGLDALRALA---EDPDLPIMAHPAFAGALSRSPDYGSHFLLLGKLMRLAGADAVIFPGPGGRFP 295

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 347546335  81 GEREVTLGFVDlmrdayiekdrsrgvYFTQDWCGLAGTMPVASG 124
Cdd:cd08205  296 FSREECLAIAR---------------ACRRPLGGIKPALPVPSG 324
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 17-71 1.30e-03

Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions. The specific function of this subgroup is unknown.


Pssm-ID: 173972  Cd Length: 406  Bit Score: 36.90  E-value: 1.30e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 347546335  17 GFTANTSLANYCRdngLLLHIHRAMHAVIDRQRNHGIHFRVLTKALRMSGGDHLH 71
Cdd:cd08207  248 GLSGLAALRRHSQ---LPIHGHRNGWGMLTRSPALGISFQAYQKLWRLAGVDHLH 299
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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